What's New in SGD in 1996

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Contents

December 10, 1996

  • Combined Physical and Genetic Maps of S. cerevisiae: The current data from SGD about both genetic and physical mapping are now available in the familiar, side-by-side format. The genetic mapping data is based on tetrad analysis results submitted to SGD and to Dr. Robert Mortimer. The physical mapping data is based on the results ofthe systematic sequencing effort. Each mapped locus is hyper-linked to its SGD locus information page.
  • Global Gene Hunter: This new tool will let you search for a gene name in SGD, Medline and GenBank. We initially developed this tool to simplify the searches researchers should perform before they submit a gene name registration, but many other uses can easily be imagined.

November 20, 1996

  • RETRIEVE AMINO ACID SEQUENCES: SGD has added a "Protein translation" option to the DNA Sequence Retrieval Form. This provides a simple way to obtain the animo acid sequence of a gene in GCG format. For an example, see the Sequence Retrieval for YHR023W.

October 25, 1996

  • DEFINE CHROMOSOMAL FEATURES DISPLAY: This page allows you to view the genetic features (ORFs, centromeres, etc) of any region of a S. cerevisiae chromosome in a graphic or a table form. Using this form, you can decide the endpoints of the sequence to be displayed.
  • DNA SEQUENCE FINDER: SGD has developed a new method of finding sequences in our database. The "Sequence Finder" allows you to browse sequences or to search for specific sequences. You can also define the coordinates of a chromosomal sequence you would like to display. Sometimes, this method is easier to use than the standard SGD search function.
  • HOME PAGE SUMMARY: We have created a summary of all the features offered on our home page. The "Home Page Summary" explains the types of data available,and the methods of accessing them. You can find the summary of each home page topic by clicking on the red question marks listed after that topic on the homepage.

October 4, 1996

  • S. cerevisiae GENOMIC VIEW: Since a picture is worth a thousand words, SGD now provides a graphic display of all sixteen chromsomes. Each chromosome is "clickable" and gives you the ability to display, in a picture form, a large region of the chromosome with all its genetic features (named genes, ORFs, centromeres, tRNAs, etc). Each genetic feature is a hyperlink to the locus page of that feature.

September 25, 1996

  • SGD'S HOT TIPS: SGD introduces a new service that provides users with periodic mini-tutorials showing how to use this database as well as other internet services. These tips will be aimed at both novice and expert users of SGD and will usually show a step-by-step process of retrieving information.

September 18, 1996

  • RELEASE OF SACCHDB VERSION 4.6: SGD has made available a new public release of SacchDB using the ACEDB software (version 4.3) developed by Richard Durbin and Jean Thierry-Mieg. This database is called SacchDB version 4.6 and is available for Macintosh and a variety of UNIX systems. Although SGD recommends using the WWW version of our database (it is more frequently updated and contains information that is unavailable in SacchDB), there are users who prefer using SacchDB to the WWW version. To download a copy of the SacchDB database, use Anonymous FTP with genome-ftp.stanford.edu (SacchDB) or ncbi.nlm.nih.gov (repository/SacchDB). Please retrieve the README.installation text file to decide which database archive files you will need for your particular system. If you have a previous SacchDB version, you should remove that version and completely reinstall version 4.6.

September 3, 1996

  • ORF DNA SEQUENCE DATASET: We now offer a set of DNA sequences of all ORFs defined by the systematic sequencing effort for use in both BLAST and FASTA searches. Note that introns have been removed from this dataset. As is true for the "Translated ORFs" dataset mentioned below, the dataset is available as a pull-down menu option (ORF-Coding) from the SGD BLAST and FASTA pages or via anonymous FTP in the /pub/yeast/yeast_GenBank folder. The file is entitled yeast_coding.fasta.Z.

August 19, 1996

  • "TRANSLATED ORFS" BLAST AND FASTA DATASETS: SGD has added a new dataset for BLAST and FASTA searches that includes the translations of the 6156 ORFs defined by the genomic sequencing effort. This dataset is available as a pull-down option in the BLAST and FASTA pages. The BLAST and FASTA results will directly report the names of the ORF(s) found in a search. In addition, the translated ORF dataset is available as text via anonymous FTP. The FTP files are named yeast_orfs.fasta and yeast_orfs.fasta.Z (for the compressed file).
  • UPDATED ALIASES: SGD has added 505 gene name aliases for known yeast genes. These secondary names were found in the Yeast Protein Database. General information about gene names can be found in the SGD Gene Registry.
  • BIOCHEMICAL PATHWAYS: A compilation of biochemical pathways, with S. cerevisiae enzymes, the names of genes and/or ORFs encoding them, substrates, products, cofactors, activators and inhibitors has been added to SGD. All of the biochemical pathway information is cross-referenced and can be browsed in the Enzyme, Metabolite, or Pathway classes of the database. When a gene or ORF is known or suspected to encode an enzyme, a link to the enzyme is available in the Locus page.

August 4, 1996

  • ORF INFORMATION TABLE: SGD has produced a table including all open reading frames (ORFs) named by the systematic sequencers of the yeast genome. The information in the table includes ORF standard name, gene name (if known), the chromosome on which the ORF is located, the chromosomal coordinates of the ATG and STOP codons of the ORF, the number of introns contained within the ORF, and the coordinates of the exons within each ORF. The ORF Locations Table for both the whole genome and for individual chromosomes is available via anonymous FTP as a tab-delineated file. This file has been replaced by the chromosomal_feature.tab available on the FTP site.

August 2, 1996

  • SACCH3D: Sacch3D is produced by SGD and presents structural information about yeast proteins. Sacch3D offers text, graphics and interactive three-dimensional images relating to the structure of yeast proteins and their homologs. New features of Sacch3D can be found listed in Sacch3D News.

August 1, 1996

  • DESIGN PRIMERS: SGD provides a program that will design sequencing and PCR primers using your DNA sequence or the S. cerevisiae genomic sequence as a template. The Web Primer program provides default parameters (i.e., Tm, GC content, endpoints), but all can be modifed.
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